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- PDB-6y1s: Bicyclic peptide bp70 in I4132 at 1.0 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 6y1s
TitleBicyclic peptide bp70 in I4132 at 1.0 Angstrom resolution
Componentsbp70
KeywordsANTIBIOTIC / Antimicrobial / Bicyclic / Lectin
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.04 Å
AuthorsBaeriswyl, S. / Stocker, A. / Reymond, J.-L.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
Citation
Journal: Rsc Chem Biol / Year: 2021
Title: A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography.
Authors: Baeriswyl, S. / Personne, H. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.L.
#1: Journal: Rsc Chem Biol / Year: 2021
Title: A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography.
Authors: Baeriswyl, S. / Personne, H. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.L.
#2: Journal: Chemrxiv / Year: 2021
Title: Mixed Chirality alpha-Helix in a Stapled Bicyclic and a Linear Antimicrobial Peptide Revealed by X-Ray Crystallography.
Authors: Baeriswyl, S. / Personne, H. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.-L.
History
DepositionFeb 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model / struct_conn
Item: _citation.journal_id_ISSN / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: bp70


Theoretical massNumber of molelcules
Total (without water)1,5341
Polymers1,5341
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint1 kcal/mol
Surface area1470 Å2
Unit cell
Length a, b, c (Å)55.459, 55.459, 55.459
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein/peptide bp70


Mass: 1533.839 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Bicyclic stapled peptide bp94 in I4132 / Source: (synth.) synthetic construct (others)
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 M CALCIUM CHLORIDE DIHYDRATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.6, 20% V/V 2-PROPANOL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000036 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 23, 2019
Details: COLLIMATING MIRROR (M1), BARTELS MONOCHROMATOR (DCCM), TOROIDAL MIRROR (M2)
RadiationMonochromator: BARTELS MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000036 Å / Relative weight: 1
ReflectionResolution: 1.04→39.24 Å / Num. obs: 7245 / % possible obs: 99.92 % / Redundancy: 65 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.006 / Rrim(I) all: 0.045 / Net I/σ(I): 51.2
Reflection shellResolution: 1.04→1.06 Å / Redundancy: 19.1 % / Rmerge(I) obs: 2.927 / Mean I/σ(I) obs: 1 / Num. unique obs: 2124 / % possible all: 98.58

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.34 Å22.63 Å
Translation2.34 Å22.63 Å

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Processing

Software
NameVersionClassificationNB
SHELXrefinement
XDSdata reduction
XSCALEdata scaling
PHASER2.7.16phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y13

6y13


Resolution: 1.04→39.24 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 --RANDOM
all-7230 --
obs-7230 99.92 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso max: 61.33 Å2 / Biso mean: 25.4355 Å2 / Biso min: 14.34 Å2
Refinement stepCycle: final / Resolution: 1.04→39.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms105 0 0 0 105
Num. residues----13
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.025
X-RAY DIFFRACTIONs_angle_d0.514
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.006
X-RAY DIFFRACTIONs_zero_chiral_vol0.132
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.318
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.039
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.084
X-RAY DIFFRACTIONs_approx_iso_adps0

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